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Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKF PDB ENTRY 1DKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% (w/v) PEG 6000, 5% (w/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.307 α = 90 b = 61.218 β = 105.38 c = 49.444 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2008-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9395 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 35 0.03 0.043 16.2 2.6 22172 22172 25.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 0.226 0.319 3.6 2.5 2665
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DKF 1.8 32.02 22172 21452 720 93.78 0.19875 0.19744 0.1951 0.23716 0.2362 RANDOM 29.809
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.43 -0.84 0.19 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.712 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 4.469 r_scangle_it 2.771 r_angle_refined_deg 2.7 r_scbond_it 1.75 r_mcangle_it 0.98 r_mcbond_it 0.49 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.712 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 4.469 r_scangle_it 2.771 r_angle_refined_deg 2.7 r_scbond_it 1.75 r_mcangle_it 0.98 r_mcbond_it 0.49 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1937 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 26
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling